hoxb1b homeobox B1b [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: hoxb1bprovided by ZNC
Official Full Name: homeobox B1bprovided by ZNC
Primary source: ZFIN:ZDB-GENE-980526-290
See related: AllianceGenome:ZFIN:ZDB-GENE-980526-290
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: cb249; hoxa1; Hoxa-1; id:ibd5001
Summary: Enables sequence-specific DNA binding activity. Acts upstream of or within several processes, including hindbrain development; neural keel formation; and regulation of histone modification. Predicted to be active in nucleus. Is expressed in several structures, including germ ring; mesoderm; neural keel; neural plate; and presumptive neural plate. Orthologous to human HOXB1 (homeobox B1). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: all
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Genomic context

Location:: chromosome: 12

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	12	NC_007123.7 (27124274..27142834)
105	previous assembly	GRCz10 (GCF_000002035.5)	12	NC_007123.6 (27032911..27051475)

Chromosome 12 - NC_007123.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Loss of hoxb1b together with pbx4 reverts the hindbrain to a groundstate identity, demonstrating the importance of hox genes in patterning nearly the entire hindbrain, and a key requirement for Pbx in this process. Additionally, we provide evidence that while pbx genes regulate RA signaling, hoxb1b regulates hindbrain identity through complex regulation of FGF signaling
Title: Coordinate regulation of retinoic acid synthesis by pbx genes and fibroblast growth factor signaling by hoxb1b is required for hindbrain patterning and development.
Data suggest that, in developing gastrula, Znfl1 controls developmental gene expression of Hoxb1b in embryonic posterior neuroectoderm by acting upstream of Pou5f3 and Sall4; these proteins appear to be involved in neurogenesis. (Znfl1 = zinc finger-like gene 1; Hoxb1b = homeobox B1b protein; Pou5f3 = POU domain class 5 transcription factor 3; Sall4 = spalt-like transcription factor 4)
Title: Zebrafish Znfl1 proteins control the expression of hoxb1b gene in the posterior neuroectoderm by acting upstream of pou5f3 and sall4 genes.
Data indicate that hox genes hoxb1a and hoxb1b have separate functions in hindbrain development.
Title: Targeted germ line disruptions reveal general and species-specific roles for paralog group 1 hox genes in zebrafish.
Hoxb1b regulates mitotic spindle rotation during the oriented neural keel symmetric mitoses that are required for normal neural tube lumen formation in the zebrafish.
Title: Hoxb1b controls oriented cell division, cell shape and microtubule dynamics in neural tube morphogenesis.

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General gene information

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Markers

fc42f02.y1 (e-PCR)
- UniSTS:193825

hoxa1 (e-PCR)
- UniSTS:186970

hoxb1b (e-PCR)
- UniSTS:238269

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within establishment of mitotic spindle orientation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within fourth ventricle development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in hindbrain development	IGI Inferred from Genetic Interaction more info
acts_upstream_of_or_within hindbrain development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within hindbrain morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neural keel formation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within nucleosome organization	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within otic vesicle development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of DNA-templated transcription	IGI Inferred from Genetic Interaction more info
involved_in positive regulation of transcription by RNA polymerase II	IGI Inferred from Genetic Interaction more info
acts_upstream_of_or_within regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within rhombomere 4 development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within rhombomere 4 formation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within rhombomere morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: homeobox protein Hox-B1b

Names: homeo box B1b; homeobox gene A-1; homeobox protein Hox-A1; hox-A1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_131142.2 → NP_571217.2 homeobox protein Hox-B1b

See identical proteins and their annotated locations for NP_571217.2

Status: PROVISIONAL

Source sequence(s)

BC133876

UniProtKB/Swiss-Prot

Q4PR97, Q8JH52, Q90423, Q98SH8

UniProtKB/TrEMBL

A3KNJ6

Conserved Domains (1) summary

pfam00046
Location:212 → 265

Homeobox; Homeobox domain

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCz11 Primary Assembly

Genomic

NC_007123.7 Reference GRCz11 Primary Assembly

Range

27124274..27142834

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_021480022.1 → XP_021335697.1 homeobox protein Hox-B1b isoform X1

UniProtKB/Swiss-Prot

Q4PR97, Q8JH52, Q90423, Q98SH8

UniProtKB/TrEMBL

A3KNJ6

Conserved Domains (1) summary

pfam00046
Location:212 → 265

Homeobox; Homeobox domain
XM_005156267.4 → XP_005156324.1 homeobox protein Hox-B1b isoform X1

See identical proteins and their annotated locations for XP_005156324.1

UniProtKB/Swiss-Prot

Q4PR97, Q8JH52, Q90423, Q98SH8

UniProtKB/TrEMBL

A3KNJ6

Conserved Domains (1) summary

pfam00046
Location:212 → 265

Homeobox; Homeobox domain
XM_021480024.1 → XP_021335699.1 homeobox protein Hox-B1b isoform X1

UniProtKB/Swiss-Prot

Q4PR97, Q8JH52, Q90423, Q98SH8

UniProtKB/TrEMBL

A3KNJ6

Conserved Domains (1) summary

pfam00046
Location:212 → 265

Homeobox; Homeobox domain
XM_021480023.1 → XP_021335698.1 homeobox protein Hox-B1b isoform X1

UniProtKB/Swiss-Prot

Q4PR97, Q8JH52, Q90423, Q98SH8

UniProtKB/TrEMBL

A3KNJ6

Conserved Domains (1) summary

pfam00046
Location:212 → 265

Homeobox; Homeobox domain
XM_005156266.4 → XP_005156323.1 homeobox protein Hox-B1b isoform X1

See identical proteins and their annotated locations for XP_005156323.1

UniProtKB/Swiss-Prot

Q4PR97, Q8JH52, Q90423, Q98SH8

UniProtKB/TrEMBL

A3KNJ6

Conserved Domains (1) summary

pfam00046
Location:212 → 265

Homeobox; Homeobox domain
XM_017358429.2 → XP_017213918.1 homeobox protein Hox-B1b isoform X1

UniProtKB/Swiss-Prot

Q4PR97, Q8JH52, Q90423, Q98SH8

UniProtKB/TrEMBL

A3KNJ6

Conserved Domains (1) summary

pfam00046
Location:212 → 265

Homeobox; Homeobox domain